

 Second example of TranSIESTA
==============================

Look at the structure in 00-Chain and in this folder.

What are the differences?

You should realise that this system is not periodic, hence
this system cannot be simulated using _conventional_ siesta method.

Follow the steps as prescribed in 00-Chain (in this case the fdf file is
the same). The step 1) below has all the steps concatenated in a single
step, without explanations.

1) 
  Run the electrode
  $> cd elec
  $> transiesta < elec.fdf | tee elec.out
  $> cd ..
  $> transiesta < chain.fdf | tee chain.out
  $> tbtrans < chain.fdf | tee chain.tbt-out

2) Plot the transmission from the perfect chain and for this
   chain. 

   How do they differ?
   
   Why is this difficult to simulate in siesta? And if you would
   do it, how would you create the siesta structure?
    HINT: The electrodes are infinite, draw the transiesta structure
          and extend the structure with infinite electrodes.

